Lily, The Doctor's Daughter
by Humanities.Best
Summary: She was an orphan with nobody to care for her, He was the time-traveling spaceman who blew up her orphanage and the alien nuns with it. What happened next, would change both of their lives forever. The Doctor adopted Lily in a desperate attempt after loosing the Pond's. Little did he know that his life would be far more different than ever.


**Please, if you were this wonder. This light. Who helped me write this. Tell me. Contact Me. I just want to thank you. Thank you for being my friend when I didn't have any. Thank you for being the Tyler to my Marcus, the Lily to My Doctor, the wonderful Padalecki child to my Conner. And if you know her. If you can find her. Please. I'm sending this out across. Share it to Tumblr, or Instagram, Twitter whatever. Please. All of you wonderful people out there. Would you find this lovely writer. Also, I may or may not continue this. Please let me know if I should transcribe any more. Thanks, Fly.**

* * *

"I'll do it.. I'll try.."

"You sure?"

"The worst is death what do I have to lose?" Jack stepped beside him and put a hand on his shoulder.

"Doctor... You have her to lose, and yourself..."

"But that's worse case Jack... You aren't looking at the bright side." He fake smiles at him. Jack does the same.

"Then ignore me." He starts leading The Doctor back to the med-bay. "And do this." The amount of blood on that cloth he had given his daughter Lily, had nearly tripled.

"If I don't see you again Jack... Thanks for everything." He smiles and hugs him. Jack smiled.

"You're welcome." He patted the doctor on the back and walked back to the console, leaving him to his business. The Doctor goes into the room and goes straight to Lily. He looks her over at the damage he caused.

"Lily... I love you." He kissed her forehead before placing his hands on her stomach. He started to remove his DNA glowing energy was going into him. The Doctor fell to his knees putting it back into him was slowly killing him. She nearly screamed as he did it, because it was literally tearing her apart. Lily saw him fall and ripped the cords connecting her to the machine and got to her knees in front of him.

"Dad... Dad, please be ok..."

"Shh..." He looked in her eyes. The Doctor placed his hands on her temples, he pressed his forehead against hers. "Your gonna be fine my love..." He then went Searching through her mind her showed her memories, of them. Then he showed her his. As this happened he was sucking the remaining energy out of her. She could see them, but she didn't know why he was showing her. Would she lose them? She shut her eyes and focused on them to distract her from what was really happening.

He was distracting her from what was happening to him. His remaining life force to keep her happy and to show his love for her. The Doctor broke away curling up in a ball, his hands in his hair pulling desperately at it like it would help.

"Dad... What's wrong?" She wanted to cry; she couldn't stand to see him like this.

"I saved you." He mumbled over and over in his ball, and his grip was weakening, his body fell to the floor with mere moments left in him. She moved over beside him, so they could see each other's faces.

"Please... You have to be ok..."He reached his hand out for her.

"Don't worry about me.. You have a full life to live." A tear fell down her cheek as she took his hand inbetween hers.

"Y-You can't leave me... You promised..." He reached his other hand up slowly and desperately with what remaining strength he had, wiping the tear off her cheek before his hand hit the floor with a loud smack, and a wince on his face.

"L-Lily... Your old enough... Y-You know my... first rule d-don't you?" He gazed into her eyes you could see straight into his soul the lost Raggedy man who stole a box and ran away.

"Of course I know, but.." Another tear fell. "...but you just can't go..." His breathing slowed, as did the beating of both his hearts. Their normally fast upbeat rhythm was a slow 4 beat ballad.

"I know i don't want to go either..."

"Please..." She was in tears at this point. Her hands held his face gently.

He had a few tears go down his cheeks.

"I-I'm sorry... I-I'm so s-so sorry." She shook her head.

"You can't... Don't go..."

"L-Lily.." The Doctor then knew he was on his death bed for he started seeing the people he loved. "Amelia..." He breathed heavily out saying her name. He saw the little girl this face first saw, her coat hat and scarf standing on a suitcase, holding hand in hand with his grown up Amy, beside her was Rory, her Roman. "River..." He saw his wive sitting on another med-bay bed wearing the dress she wore the last time they met when he took her to delirium to see the singing towers. "Hello Sweetie." She whispered. The Doctor saw Donna in her pinstripe suit with her grandad Wilf they looked at him smiling. Martha and Mickey were there too watching over him. "Rose.." He muttered with a sweet tone with hurt pain and despair in it. There she was and grinned her teeth-tongue smile, wearing the Union Flag top he loved seeing her in. She bent down beside him along with Amelia and River. Sarah Jane walked in from the hall. A young and perky journalist who smiled and stood next to River. Jack was there too, in his long coat, holding hands with Clara. Jenny was next to them smiling. "Hello Dad." The whole room was filled with the people he loved. But they faded. All except Rose and Amelia. They stood up and looked at each other. "No.. Please don't go.." The simply shook their heads and split apart revealing Lily as a child. When he first saw her, the daughter he loved. But she faded and he saw the real Lily. Amelia and Rose were sat beside her, and his breaths drew short, and his eyes were closing slowly. When they finally closed, and he whispered "Goodbye" with his last breath.

* * *

 **Twelve Years Ago...**

Lily ran up to the window of the orphanage, watching all her friends leave. They had all gotten adopted, all but her. The Sisters in the Abby were nice and all bit she wanted parents. A Mom and a Dad, maybe sisters or even a brother. But right now she didn't want to think about that. Lily was scared, and she had all the right to be. The past few nights she had been hearing strange noises coming from her walk in closet that the girls shared. Allysa her best friend heard them too, but today she was adopted. Lily would never see her again. Her only friend gone. Lily had informed the Sisters about the noises, but they thought it was fairy tale made up for attention. Now she was left to face it alone. When night fell she stalled as long as she could with getting ready for bed. Then she prayed, longer than she had ever prayed before. Lily climbed in bed and sat with her eyes open watching snow fall outside the window. She had just about fallen asleep when the noise starting scratching at the door.

The growling whining sound that wouldn't leave her alone. Lily managed out a scream but nobody came. All was silent in the halls of the Abby. The noise filled her head as she screamed again. But this time a funny man in Tweed, and a bow-tie came flying in. With a mop of brown hair on his head.

"It's alright." Where his first words. In an English accent of all things. Before she knew it, they were running down the halls of the Abby, and then made it outside. The Abby exploded, her whole world gone in one moment. This strange man. The Doctor he called himself adopted Lily. He didn't know who to take her to. The Doctor became her father. He never traveled in the Tardis, he kept it hidden away. Lily knew he was an alien, but he never told her anything else. On her sixteenth birthday she saw the Tardis, and they were off. Never living on Earth again.

* * *

 **Six Hours Earlier...**

The Doctor for her twenty second birthday took her to the planet Antar. Hoping they could have tea with the queen. But Daleks reigned there. In an effort to save her father she was shot by a Dalek. The Doctor gave up a regeneration to heal her. Lily was fine for a bit. That's when they met Captain Jack. He noticed how Lily wasn't normal. The human Timelord DNA was not compatible, and now Lily was dying.

* * *

 **Present Day:**

"Goodbye.." She tells him in a soft, kind voice. Lily looks into the fading eyes of the only parent like figure she had. He'd been there for her when no one else was. The lost little girl with no one to love. Just a single tear slipped down her cheek as she took a few steps back. Still in tears, she told him,"Thank You." His body lay there limp and unmoved. The room was dead silent. She couldn't stay there. Lily ran out of the room and down to her bedroom. Going in, she shut the door and slumped down against it. With her face in her knees, that were brought up to her chest, she cried. Jack saluted the body and smiled at him one last time before going off to find Lily. The Doctor laid on the floor motionless, but his mouth opened and a whisp of golden breath came out. She shouted things to herself; some that made sense and some that really didn't. Now she already felt alone, not caring if jack was there or not.

Jack understood what she was going through. He had lost his lover, his wife, his daughter, and his grandson. Almost All because he couldn't die. He knocked on the door gently. She moved to the side so her back was to the wall. She really was blaming this on herself. If she wouldn't have stepped infront of that dalek, this wouldn't have happened. Lily choked back tears before answering to the knock. "Y-Yes?"

"It's Jack... Can I come in?" He asked politely ready to back away if she needed her space.

"Yeah..." She nodded but he didn't see that. Though, she still sat with her legs brought up and her face buried against her knees. He opened the door a crack and came in and sat on the floor in front of her. For a while, she was still the same as before Jack came. It was about half an hour til she actually looked up at him, with her tear stained eyes.

He sat crossed legged on the floor in front of her. "I'm here when your ready." She nodded.

"I'm ready." She now sat cross legged.

"Okay... Say what you need to say and get over it."

"I just feel like its my fault because if I wouldn't have wanted to do something dangerous, then I wouldn't have felt the need to let that dalek shoot me instead of him. It could have shot him and he could have regenerated and he wouldn't be dead. He wouldn't have had to waste his last regeneration on me and have it not really work anyways. I mean... I know you'll be here for me if I need it, but I feel so alone. Until he took me in, nobody cared. If I'd died before that, there would have been no one to care. For so long, he was the only person who loved me and who cared. I just don't know how I'll get on with things of he's not here."

"That's what i though after he left me.. How could I go on after traveling across the universe? But i did i settle down i married i had a daughter. But i had to let them go i was to dangerous for them. I moved away. I fell in love again. But he died saving me... Lily you see... I cant die... The Doctor and I's friend did a wrong thing because she loved him. That made me immortal... I have every one i love die Lily. But you haven't seen every thing yet. You can still fall in love and settle down. Trust me you'll be fine."

"I know... But it's not easy. I can't just go right now-" She stood. "Just... I need a moment alone." Lily grabbed something off the desk and left the room, walking down the hallway. Jack was only telling her what was true, but it's not what she wanted to here. She stopped at the med-bay and walked in. Stopping beside his body, she kneeled down and took something from her pocket. It was a photo of them together from a year or two ago. The Doctors body laid moved slightly but to her she would not have noticed. And she didn't notice. Lily took the picture and tucked it in his pocket, then leaning down and kissing his forehead. "Do me a favor, Dad... Please don't be dead..." She spoke quietly. Another whisp of golden air came from his lips. Then his body was still. She saw that little whisp but thought nothing of it, in fear it meant nothing. Lily stood and walked out; the picture poked out of his breast pocket. The Doctor breathed out another large whisp before he eyes bolted open and he gasped for air.

"What the?" She heard the gasp from down the hall a bit and rushed back down there, only to find him alive.

He beat his chest trying to get his other heart to start, gasping loudly. Lily felt bad for doing so, but she left and went back to Jack. "There's something you should see." He hit his back and it finally started.

"Badaboomba!" The Doctor tried to stand but he couldn't feel his legs. He scrambled to the counter and pulled himself up to look in the mirror. Meanwhile Jack said.

"What? Is something the matter?"

"Not exactly." As she led him to the med-bay, she spoke. "He's... Not exactly dead anymore..." The Doctor fell down and was dragging himself to the med-bay door. Lily didn't wait for a reaction and walked quicker to him. When she saw him struggling, she bent down and stopped him. "It's alright... You don't need to go anywhere." He smiled, at her touch, but frowned wanting to keep going.

"I don't know whats wrong with me." She smiled and helped him up, sitting him on the bed.

"It's ok. We don't need to know right now."

"Doc the universe can wait a bit for you to heal." Jack said after he arrived in.

"But I-I died.." The Doctor mumbled. He smiled vaguely as his body was restarting it self. His hearts returning to a steady beat. He could clearly see the thing she'd left in his pocket.

"Let's just be glad you're not dead." Lily stated. He could see it but he didnt pay attention til now. The Doctor pulled it out and studied the photo. "I, uh... Thought you were dead so I left it with you... So you could always remember me." He smiled and kissed her forehead.

"I could never forget you." She stayed with him a while before going to the doorway.

"You just stay here. And try not to hurt yourself." Lily left the room and walked out to the console. He didnt listen he slid off the bed and walked crookedly down the hall, for all the feelings had still not come back to his legs. Jack had gone to find something that would help the Doctor. She walked up to it and "un-stalled" them, pushing some buttons and pulling a few levers. She flew it, much gentler than the doctor always did. He stumbled a bit through the hallways and found his way to his room. She landed it in London, and walked out, locking the door from the outside. Lily walked down the street, and in a little cafe. He was scanning himself with his screwdriver and then dug under his bed for something. In about an hour, she came back to the Tardis. He had found some ancient time lord medicines in a wooden box. She'd brought him back some hot tea. Lily walked down the hall and knocked gently on his door.

"Yeah?" He said muffled from under his bed.

"I stopped at a cafe and got you some tea... Do you want it?"

"Tea? Yes please! Leave it on my dresser. Because his room was a mess, like it was ever clean.

"Ok." She just popped in and set it on his dresser. Before leaving, she said,"I'll just be wandering around. Call if you need me." And she went.

"Thank you Dear!" He called after he and brought up a box of stuff dust covering his hair. Lily wandered for a while, checking out different places she hadn't seen. He stumbled out of the room and went into a storage room where he kept keepsakes from past adventures. She found the swimming pool and decided to get in. So... She put on her bathing suit and dived in. He managed to find a pain reliever and was fine. He went back to his room and was drinking the tea while somewhat cleaning. She at one point just sat in the water, relaxing. He finished and then wandered around the Tardis.

Lily swam some laps before just sitting there again. He peeked and saw her in the swimming pool, and grinned. She didn't notice him and dived underwater. He watched for a bit before leaving. She only noticed when she came up for air as he left. He smiled and went down the hall straightening his bowtie with dust still in his hair. She got out and dried off, getting dressed again. Lily put her hair in a French braid and started walking back to the console. He made his way back to the console, eventually a little bit before her. She walked in when he had already been there and started doing something on the console. "Have a nice swim?"

"Yes." She flipped a few switches. He smiled, and was messing with something on the screen. She set the Tardis off, taking it to America. He helped her a bit flipping some that were by him but his main focus was on the screen. When they landed, she left. He watched and dusted his head off before sticking it outside the door. She'd disappered down the street already. He looked around and went outside. They were in California, the place they'd lived two years. Lily was taking Jack's advice: fall in love. The Doctor walked around seeing how the area had changed and he stopped by their old house.

She walked around, past the beach. Lily eventually met with some friends she'd had while they lived there and they went down to the beach. He went and stopped and cafe getting some more tea before going into little shops. Lily surfs for a little while, herself not being that bad for her first time. The Doctor had found a hat shop, looking for a fez, and he found one, and bought it wearing it around town. Lily was sitting on the sand, her dark brown hair now in a side braid, after getting out of the water. A guy walked over and sat beside her.

"You're not that bad out on the waves," he began,"is it your first time?" She looked over at him.

"Yeah... It is." The Doctor wore the fez around eventually meeting up with Jack who about died of laughter when he saw him. They'd gone down to a club, though she wasn't exactly dressed for it she went anyways. Lily and them were sitting at the bar, having a few drinks. Jack wanted to take them to a bar but the Doctor refused. They walked around a bit before he eventually got him to go sky had fallen dark outside. Lilys friends had probably two or three drinks each, herself drinking wine instead of beer. That really wasn't much better. It was basically a nightclub, or that's how people made it. So they all went to the dance floor, her hair down now. They sat up at a booth talking about some adventure the Doctor not really wanting to drink, though Jack did but he got the doctor to get down almost a whole bottle of Brandy. Lily danced to the music, eventually going back to sit at the bar again, which was right across from the doctor and jack; quite nearly. Lily talked to them, over the course of another glass of wine.

The Doctor could usually drink and drink with out getting drunk because of his genetics, but he had still not fully recovered from his accident a while back. When she drank, it didn't matter how much, she was wasted. They all left quite soon, but not before she downed two more glasses. He was gone and so was Jack they paid and left the bar singing and stumbling down the street. She was so wasted she could hardly see straight, with quite blurry vision. Lily made it back to the TARDIS after an hour, nearly falling 10 times on her way. When she opened the door, which took her 7 minutes after fumbling with the key, and stumbled in; leaning against the door once she was in. They fell at least 10 times on one block before they got to the Tardis. The Doctor tried to snap his fingers but he couldn't manage to do that. Jack and him started singing in Italian really loud before the got the door to open. Surely he wouldn't care she was totally wasted because he was too. When they walked in she spoke to them, clearly tipsy with her words slurring.

"Hey guys!" They both did too.

"L-Lily. Why are you drunk?" Jack laughs and stumbles to the console. "You know when you say your name over and over it starts to sound like it can't be true." The Doctor laughed and looked at Jack. "Doc-tor... Doctor... Doctor."

"Well... I met old friends, went to the beach, went to the nightclub..." She shrugged and laughed. "...And had maybe 10 huge glasses of wine..." She signaled with her hands the size of large glass. "Like... This big!"

"That's Huuuuuge!" Jack shouted. The Doctor laughs. "Try it seriously guys. Doctor...Doctor." Lily pulled out a wine bottle and laughed.

"Probably like fffffour times this amount." She opened the bottle and chugged almost half of it.

"Aww Liiiiiily share with usssss!" Jack stumbled over to her.

"I had enough." The Doctor said childish. "But I want more!"

"Nooooope..." She stepped away, light on her feet; and drank the rest.

"Awwwww... Your mean..." Jack stumble-stomped down the hallway because he was "mad" at her. The Doctor took the bottle away and placed it on the console.

"Noooooo mooooorrrre."

"Heeeey..." She looked at him. "I wasn't dooooone with that..."

"Nooooo Moooorrrre!" He tried to sound tuff like a Dad but he just started laughing. She swiped the bottle and finished it off before he could do anything. He didn't have fast reflexes anyway so he couldn't have. "Go to your room!" He said trying to keep a straight face.

"You caaaan't make mmmme." She crossed her arms over her chest.

"Yeah i caaaaaan'a!"

"Thhhhhen do it!"

"I have. Timelord body. I Caaan consuuuume more alcholllll than youuuu. But huuuuuumansss are pathetic yoooou pass out eventually after enoughffff."

"Then maaaaaybe you should lettttttt me haaaave more... Sooooo I can passssssss out."She waved him off and stumbled down the hall, passing out on the floor before getting to her room.

"Seeeeeeee! Hehehehe!" He laughed and walked down the hall and picked her up almost dropping her pulling her into her bed before going to his own room and passing out. She slept til 11am the next day, throwing up twice. But before anyone noticed, she was dressed and out the TARDIS doors again. She met her friends at the beach again. The Doctor was fine no hangover. He was just had a headache. Jack though was sick and the Doctor was taking care of tried surfing again, and it worked out better than the day before. When she was sitting on the sand, the same boy from yesterday came over. "You know..." He began. "You never told me your name." The Doctor went out with his Fez and was getting somethings Jack wanted.

"You never asked." She said recognizing the voice, and smiled over at him.

"Fine. What's your name?" His head turned to look at her.

"Lily." She answered. "And what about you?"

"Connor," he responded. The Doctor came back to the Tardis made Jack some tea, and gave him aspirin.

"Well Connor-" She was cut off by him.

"Why don't you come with us to dinner? The other guys over there and some of your friends were gonna go, so.. I thought you'd like to come."

Jack was getting better and the Doctor fell asleep in a chair. She ended up going with them, and giving her phone number to Connor. Lily didn't come back to the TARDIS til almost midnight. They'd gone to the club but this time she'd only had two glasses. The Doctor met her at the Door because he didnt usually need sleep but he slept longer than he had in years he was fully rested and ready to go. Since it had been only two, well... Basically three, she wasn't wasted, just a bit off.

"And where on the bloody Earth have you been til wee hours in the morning?" She walked past him.

"At the beach... And then at the club."

"With who?" He asked and then turned around shutting the doors.

"Friends." She gave him the most open-ended answers.

"Your... Hiding something from me... it was more than friends. Im a master at lying so i should know."

"They really are only friends." She started to walk down the hall.

"Promise me?" He asked leaning against the console.

"I promise." She went to her room and laid down.

"Women.. You just can't get through to them..." He mumbled. The next morning she was up at 10, Connor wanting to meet her down at the beach. She went to leave, but got stopped by the doctor at the door. "And where might you be going Mrs. Socialite?"

"To the beach." He looked in her eyes searching for the truth and he let her go. Lily shut the door and left, actually meeting Connor on the walk there. They sat on the beach together, before they both got on his surfboard. The Doctor followed her there much to the dismay and advice Jack gave him. He wore shades and a Stetson and stayed pretty far away. It rested not that far out in the water as they sat on it. She was in front of him, him behind with his legs around hers, and his arms around her too; oddly it was like how a couple would be sitting, but they were only friends.

"Did I ever tell you that you're cute?" She smiled and let out an adorable laugh.

"No... But you implied it." The Doctor watched glaring eyes staring at them, a bit like an overprotective father. Well that's what he was. Conner spoke again,

"Well I'm telling you know, I think you're beautiful." His chin gently rested on the top of her head. She was leaned back against his chest; he wasn't wearing a shirt, being that they were in the water. The Doctor watched furious because she had been keeping him a secret from himself. It only had been three days since they met. They really weren't a couple, at least not yet. He dipped his head forward, kissing her on the neck. She leaned her head up to look in his eyes. It was ok they were like this because there was only about 1 person there, plus they were on a more isolated part of the beach. He stormed of to the Tardis and was searching through the database. Lily and him went back to the sand, and it was probably an hour before she left. He was looking up the boy he saw. She came back another hour after leaving the beach. Lily could tell the Doctor was angry.

The Doctor was making sure he was human and not have a criminal record, with fire and fury in his eyes finding out that he was perfectly human and free of a criminal record. She'd came in the door without a sound, so he didn't notice. She started to walk down the hall. The Doctor didn't notice the door open, or walk down the hall. He was under the console digging something out. Lily went down to her room, and sat on the bed, door cracked open. She talked on the phone to Connor, before walking back out to the console. The Doctor was curled up inside a cupboard shelves looking at pictures of them. He heard her talking he was still mad but also kinda sad. She'd come down to the console room after getting off the phone. What she was doing? Even she didn't know. He heard her above him and stayed where he was. She sat in the console chair, just kind of sitting there thinking. He listened from above before getting on with what he was doing. Lily walked down there.

"There's something I want to tell you Dad."

"You found me how?" The Doctor looked up a sad gaze in his eyes.

"Its your thinking spot. You come here when your troubled or sad... Anyway. I have a boyfriend."

"Oh? And when did you plan to tell me this?"

"Today.."

"When did you meet him?"

"Three days ago." He sighed and looked up.

"Okay... Eventually im going to meet him right?"

"Yeah... I don't know when though.. I can't exactly bring him here.."

" We can meet at a neutral location"

"Probably..." She walked back to her room. The Doctor sighed and watched her leave. Once in her room, she called Connor. He went up to the console and moved the Tardis to an empty lot a little bit away from where they were. She didn't care. She explained everything to him. The whole TARDIS thing and such. But really, he seemed perfectly ok with it. He temporarily fixed the Chameleon Circuit and the Tardis looked like a house, he rearranged the interior also like a house just for her and her boyfriend. She walked out to where the console should have been. But was surprised to find it completely rearranged. And the Doctor looked more normal than ever.

"Hello." He said with a quirky smile.

"Hello Dad." She answered with a grin.


End file.
